Nickel in PDB 5dav: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxydehydrocyclopeptin

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxydehydrocyclopeptin, PDB code: 5dav was solved by M.Groll, A.Braeuer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.050, 120.770, 66.660, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.6

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxydehydrocyclopeptin also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Potassium	(K)	1 atom

The binding sites of Nickel atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxydehydrocyclopeptin (pdb code 5dav). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxydehydrocyclopeptin, PDB code: 5dav:

Nickel binding site 1 out of 1 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxydehydrocyclopeptin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxydehydrocyclopeptin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:20.1 occ:1.00 OD1 A:ASP136 2.2 17.8 1.0 O3 A:TRS403 2.2 27.9 1.0 NE2 A:HIS211 2.2 19.4 1.0 NE2 A:HIS134 2.3 18.4 1.0 N A:TRS403 2.4 28.4 1.0 O1 A:TRS403 2.4 23.0 1.0 C A:TRS403 2.8 27.3 1.0 C3 A:TRS403 2.9 27.4 1.0 C1 A:TRS403 3.1 26.4 1.0 CG A:ASP136 3.1 18.3 1.0 CE1 A:HIS211 3.1 18.8 1.0 CD2 A:HIS211 3.2 19.1 1.0 CE1 A:HIS134 3.3 17.9 1.0 CD2 A:HIS134 3.3 18.4 1.0 OD2 A:ASP136 3.3 19.1 1.0 ND1 A:HIS211 4.2 18.4 1.0 CG A:HIS211 4.2 18.9 1.0 C2 A:TRS403 4.3 27.4 1.0 ND1 A:HIS134 4.3 17.7 1.0 OE1 A:GLN131 4.4 19.8 1.0 CG A:HIS134 4.4 18.2 1.0 C8 A:58J402 4.4 21.1 1.0 CB A:ASP136 4.5 17.3 1.0 C9 A:58J402 4.7 21.8 1.0 O2 A:TRS403 4.8 26.2 1.0 CA A:ASP136 4.9 16.7 1.0 N A:ASP136 4.9 17.0 1.0

A.Brauer, P.Beck, L.Hintermann, M.Groll. Structure of the Dioxygenase Asqj: Mechanistic Insights Into A One-Pot Multistep Quinolone Antibiotic Biosynthesis. Angew.Chem.Int.Ed.Engl. V. 55 422 2016.
ISSN: ESSN 1521-3773
PubMed: 26553478
DOI: 10.1002/ANIE.201507835